def set_meta(self, dataset, **kwd):
"""
for lped/pbed eg
"""
Html.set_meta(self, dataset, **kwd)
if not kwd.get('overwrite'):
if verbose:
gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
return True
try:
efp = dataset.extra_files_path
except Exception:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
try:
flist = os.listdir(efp)
except Exception:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
if len(flist) == 0:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name, efp))
return False
self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy genotype datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
for lped/pbed eg
"""
Html.set_meta( self, dataset, **kwd )
if not kwd.get('overwrite'):
if verbose:
gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
return True
try:
efp = dataset.extra_files_path
except:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
try:
flist = os.listdir(efp)
except:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
if len(flist) == 0:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name, efp))
return False
self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy genotype datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
return True
def set_meta(self, dataset, **kwd):
Html.set_meta(self, dataset, **kwd)
for fname in os.listdir(dataset.extra_files_path):
if fname.startswith("chromosomes"):
dataset.metadata.chrom_bed = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("chromosome_windows"):
dataset.metadata.chrom_windows = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("IDEAS_input_config"):
dataset.metadata.input_config = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("tmp"):
dataset.metadata.tmp_archive = os.path.join(dataset.extra_files_path, fname)
self.regenerate_primary_file(dataset)
def set_meta(self, dataset, **kwd):
Html.set_meta(self, dataset, **kwd)
for fname in os.listdir(dataset.extra_files_path):
if fname.startswith("chromosomes"):
dataset.metadata.chrom_bed = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("chromosome_windows"):
dataset.metadata.chrom_windows = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("IDEAS_input_config"):
dataset.metadata.input_config = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("tmp"):
dataset.metadata.tmp_archive = os.path.join(dataset.extra_files_path, fname)
self.regenerate_primary_file(dataset)
def set_meta(self, dataset, **kwd):
"""
NOTE we apply the tabular machinary to the phenodata extracted
from a BioC eSet or affybatch.
"""
Html.set_meta(self, dataset, **kwd)
try:
flist = os.listdir(dataset.extra_files_path)
except Exception:
if verbose:
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
return False
bn = dataset.metadata.base_name
if not bn:
for f in flist:
n = os.path.splitext(f)[0]
bn = n
dataset.metadata.base_name = bn
if not bn:
bn = '?'
dataset.metadata.base_name = bn
pn = '%s.pheno' % (bn)
pp = os.path.join(dataset.extra_files_path, pn)
dataset.metadata.pheno_path = pp
try:
with open(pp) as f:
pf = f.readlines(
) # read the basename.phenodata in the extra_files_path
except Exception:
pf = None
if pf:
h = pf[0].strip()
h = h.split('\t') # hope is header
h = [escape(x) for x in h]
dataset.metadata.column_names = h
dataset.metadata.columns = len(h)
dataset.peek = ''.join(pf[:5])
else:
dataset.metadata.column_names = []
dataset.metadata.columns = 0
dataset.peek = 'No pheno file found'
if pf and len(pf) > 1:
dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
else:
dataset.metadata.pheCols = [
('', 'No useable phenotypes found', False),
]
if not dataset.info:
dataset.info = 'Galaxy Expression datatype object'
if not dataset.blurb:
dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
NOTE we apply the tabular machinary to the phenodata extracted
from a BioC eSet or affybatch.
"""
Html.set_meta(self, dataset, **kwd)
try:
flist = os.listdir(dataset.extra_files_path)
except:
if verbose:
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
return False
bn = dataset.metadata.base_name
if not bn:
for f in flist:
n = os.path.splitext(f)[0]
bn = n
dataset.metadata.base_name = bn
if not bn:
bn = '?'
dataset.metadata.base_name = bn
pn = '%s.pheno' % (bn)
pp = os.path.join(dataset.extra_files_path, pn)
dataset.metadata.pheno_path = pp
try:
pf = open(pp, 'r').readlines() # read the basename.phenodata in the extra_files_path
except:
pf = None
if pf:
h = pf[0].strip()
h = h.split('\t') # hope is header
h = [escape(x) for x in h]
dataset.metadata.column_names = h
dataset.metadata.columns = len(h)
dataset.peek = ''.join(pf[:5])
else:
dataset.metadata.column_names = []
dataset.metadata.columns = 0
dataset.peek = 'No pheno file found'
if pf and len(pf) > 1:
dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
else:
dataset.metadata.pheCols = [('', 'No useable phenotypes found', False), ]
if not dataset.info:
dataset.info = 'Galaxy Expression datatype object'
if not dataset.blurb:
dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
return True
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('chromosome_windows.txt',
description='Chromosome window positions',
is_binary=False,
optional=True)
self.add_composite_file(
'chromosomes.bed',
description='Bed file specifying window positions',
is_binary=False,
optional=True)
self.add_composite_file('IDEAS_input_config.txt',
description='IDEAS input config',
is_binary=False)
self.add_composite_file(
'tmp.tar.gz',
description='Compressed archive of compressed bed files',
is_binary=True)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('Sequences',
mimetype='text/html',
description='Sequences',
substitute_name_with_metadata=None,
is_binary=False)
self.add_composite_file('Roadmaps',
mimetype='text/html',
description='Roadmaps',
substitute_name_with_metadata=None,
is_binary=False)
self.add_composite_file('Log',
mimetype='text/html',
description='Log',
optional='True',
substitute_name_with_metadata=None,
is_binary=False)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('%s.pheno',
description='Phenodata tab text file',
substitute_name_with_metadata='base_name',
is_binary=False)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('%s.pheno', description='Phenodata tab text file',
substitute_name_with_metadata='base_name', is_binary=False)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('chromosome_windows.txt', description='Chromosome window positions', is_binary=False, optional=True)
self.add_composite_file('chromosomes.bed', description='Bed file specifying window positions', is_binary=False, optional=True)
self.add_composite_file('IDEAS_input_config.txt', description='IDEAS input config', is_binary=False)
self.add_composite_file('tmp.tar.gz', description='Compressed archive of compressed bed files', is_binary=True)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
def set_meta( self, dataset, **kwd ):
Html.set_meta( self, dataset, **kwd )
self.regenerate_primary_file(dataset)
def __init__( self, **kwd ):
Html.__init__( self, **kwd )
self.add_composite_file( 'Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False )
self.add_composite_file( 'Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False )
self.add_composite_file( 'Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False )
def set_meta(self, dataset, **kwd):
Html.set_meta(self, dataset, **kwd)
self.regenerate_primary_file(dataset)
def __init__(self, **kwd):
Html.__init__(self, **kwd)